There are actually four John Howletts, three from Origins (Earth-616), and one from Wolverine: The End (Earth-4011).
John Howlett Sr. is Wolverine's Grandfather, and only appeared in the Origins series.
John Howlett Jr. is Wolverine and John Howlett III's father, who appeared and died in the Origins series.
John Howlett III of Earth-616 is Wolverine's older brother, who was killed before Wolverine was born, because he was a mutant and his parents feared him. He never appeared in any book.
John Howlett III of Earth-4011 appeared in the Wolverine: The End series, where it turned out that he had survived his parents' attempts to kill him.